OK, I may have to take that back.
I just installed Naviscope (8.7 - does not seem to have been updated very recently) on my system.
I downloaded new mail in Thunderbird (1.5.0.4) I also have multiple profiles. avast scanned the downloaded mail and inserted the X-Antivirus headers in the scanned mails.
So, we may need to look for other causes.
In your Thunderbird POP accounts ... what is the port number set for the accounts you are accessing?